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DRUG DESIGN STUDY AIDS QUESTIONS.

Presentation · January 2021

DOI: 10.13140/RG.2.2.25977.49760

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 DRUG DESIGN SUBMODULE SUMMARY
Table of Contents
PART I. DRUG DISCOVERY PROCESS ...................................................................................................................................3
Q1. What bring the innovation deficit of the new chemical entities?................................................................3
Q2.During drug design process, there are targets involve in SAR, and what are they?..............................3
Q.3 Why does the drug discovery process is called the wasteful game? ..........................................................3
Q.4 List the steps of drug discovery process...............................................................................................................4
Q5.Mention the techniques used in drug target identification............................................................................4
Q6. There are step of drug target identification in risk bearing, what are they? .........................................4
Q7.What is the drugability. ...............................................................................................................................................4
Q8.differntiate hit compound from lead compounds. ............................................................................................4
Q9.Which technique is currently used in testing the validated hit (lead) .......................................................5
Q1O.Why do we need to test the validated hit or lead compound .....................................................................5
Q11.mention the techniques involve in drug target identification ...................................................................5
Q12.list the criteria fulfilled by thehit to be accepted as lead .............................................................................5
Q14. List the technique follow in modification of lead compound .....................................................................6
Q16. It is vital to conceive lead optimization as a simultaneous multidimensional process rather
than a sequential one. Explain why how? ....................................................................................................................6
PART II. DRUG DESIGN .............................................................................................................................................................7
Q17.List the drug design techniques. ............................................................................................................................7
QQ. State three different ways in which computers are used in the design of new drugs. .......................7
Q18.What are the aim of drug design?. .........................................................................................................................7
Q20. Discuss about functional group and bind role of ligand into receptor...................................................9
Q21. Which functional group should be important designing blockers drug ................................................9
Q22.It is prohibited to remove the pharmacophore group in drug design. What is pharmacophore
group? State an alternative technique may you applied instead of remove. .................................................9
Q23.list the strategies should be applied in optimizing the drug target interactions and comment on
each . ..........................................................................................................................................................................................9
Q24.1. what are the techniques or strategies can you make to optimize the access to the target?. ... 10
Q24.2. Give the technique can be performed in designing the following drugs ......................................... 10
Q25.what is QSAR .............................................................................................................................................................. 10
Q26.you are designing a drug with improving absorption then you find the functional group you
need to remove or mask involves in binding , How can you overcome this issue? .................................. 10
 Q27. Which is absorbed better than other and why ? .......................................................................................... 10
Q29.with examples, what are stereoelectronic modification? ......................................................................... 11
Q30.metabolic blockers .................................................................................................................................................. 11
Q31. List the techniques involve in metabolism improvement. Discuss each ............................................ 12
Q32.what is self-destruct drug ..................................................................................................................................... 12
PART III. DRUG TARGET ....................................................................................................................................................... 13
Q33.Discuss the following regarding drug target .................................................................................................. 13
Q35.Regarding toxicity .................................................................................................................................................... 13
Q37. What are the purposes of prodrug in both pharmaceutical drug designing and drug
formulation processes? ................................................................................................................................................... 14
Q38. All prodrug are activated by the enzyme? Explain ..................................................................................... 14
Q39. With an examples , What is sentry drug ......................................................................................................... 14
PART IV DRUG DEVELOPMENT .......................................................................................................................................... 15
Q40.What are the three main issue involve in drug development? ................................................................ 15
Q41. Regarding the drug development differentiate the chemical development from process
development........................................................................................................................................................................ 15
Q42.what is an orphan drug? ........................................................................................................................................ 16
Q43What does patent cover in drug development ............................................................................................... 16
Q44. You are analyzing the toxicity in vivo of the drug in animal. Give two sample can be used to
make analysis...................................................................................................................................................................... 17
Q45. What should you have to study in development of the drug ................................................................... 17
Q46.National Institute of Health organize the clinical trial into 5 different type, What are they??? . 18
Q47. Describes the phases of clinical trial................................................................................................................ 18
QQ. the structure of aspirin is shown below , answer the questions.............................................................. 19
QQ. What are the technique used in drug design ................................................................................................... 19
References................................................................................................................................................................................. 20
PART I. DRUG DISCOVERY PROCESS

Q1. What bring the innovation deficit of the new chemical entities?
 Increased demand on safety for drugs
 This involve in increasing the trial number then
make most drug reaching to market
 Low hanging fruit” have been picked.
 The cost taken by the drug discovery to obtain final
product

Q2.During drug design process, there are targets involve in SAR, and
what are they?

 Membrane Proteins
 Nucleic acids [DNA and RNA]
 Enzymes and Hormones
 Etc.

Q.3 Why does the drug discovery process is called the wasteful game?
Q.4 List the steps of drug discovery process

 Drug target identification

 Drug target validation
 Lead compound identification
 Lead compound optimization
 Preclinal and clinical development

Q5.Mention the techniques used in drug target identification

 Genomic : contain the automation and informatics

 Bioinformatics : based on paralog
 Proteomics : is high throughput screening
Q6. There are step of drug target identification in risk bearing, what are they?

 Hunch
 literature precedent
 cell model
 animal model
 pharmacology in animal model
 Pharmacology in human disease.

Q7.What is the drugability.

Is the strong interaction between the ligand in the receptor

depending on the comfortable 3D structure of both ligand and
receptor.

Q8.differntiate hit compound from lead compounds.

 HIT is a compound that has activity at a predetermined

level against a target (has current affinity but no current
activity)
 LEAD is compound that has currently both activity and
affinity (described as future drug)
Q9.Which technique is currently used in testing the validated hit (lead)

It is common to test for interactions using recombinant proteins

expressed in cell lines

WHY NOT ANIMAL? For safety and right of living things

Q1O.Why do we need to test the validated hit or lead compound

We carry test to determine if the lead or validated hit has the
following properties

 Selectivity versus a panel of other receptors (targets)

 Physicochemical characteristics
 Drug-like properties
 Metabolic properties (half-life etc.)

Q11.mention the techniques involve in drug target identification

 Screening
 Structure based drug design
o Crucial point for reliable high-throughput screening
results is the robustness and quality of the biological
test assays.

Q12.list the criteria fulfilled by thehit to be accepted as lead

o Pharmacodynamics properties
 EfficacyPotency
 Selectivity
o Physiochemical properties
 water solubility
 chemical stability etc.
o Pharmacokinetic properties
 metabolic stability
 toxicological aspects.
o Chemical optimization potential
 ease of chemical synthesis
 derivatization.
o Patentability
Q13.What is bottle neck in drug discovery process?

o Lead compound optimization

o At this stage, medicinal chemists conduct extensive
SARs to improve potency and selectivity.
o Also, this is the opportunity to improve
physicochemical
and drug-like properties
o The multiple test are done parallel
Q14. List the technique follow in modification of lead compound

o Molecular modeling
o Quantitative structure-activity relationships QSAR
o Structural biology (structure-based drug design) SAR

Q15.what should you do if the compound do not fulfill the requirement for
successful drug development

o Candidate have to be optimized through the synthesis

better suited derivatives

Q16. It is vital to conceive lead optimization as a simultaneous

multidimensional process rather than a sequential one. Explain why how?

Optimizing leads first with respect to pharmacodynamics

properties (potency, selectivity, etc) and looking at
pharmacokinetic parameters of these optimized compounds later
guarantees frustration in the late optimization phase
PART II. DRUG DESIGN

Q17.List the drug design techniques.

o 3D structure of biological target( receptor-based drug design)

o Structure of known active small molecules (pharmacophore-based
drug design).
o Computer assisted drug design (CADD)
o Molecular graphics
o Pattern recognition
o Receptor fit

QQ. State three different ways in which computers are used in the design of
new drugs.
 Physicochemical parameters involved in drug activity
 quantitative structure activity relationship (QSAR)
 quantum chemistry models to determine the most promising
substance of a series

Q18.What are the aim of drug design?.

o To produce the drug with:

o The drug should have a good selectivity for its target
o The drug should have a good level of activity for its target
o The drug should have minimum side effects
o The drug should be easily synthesized
o The drug should be chemically stable
o The drug should have acceptable pharmacokinetics
properties
o The drug should be non-toxic
Q19.Pharmacodynamics and pharmacokinetics should have equal priority in
influencing which strategies are used and which analogues are synthesized.
Comment?
Q20. Discuss about functional group and bind role of ligand into receptor

Q21. Which functional group should be important designing blockers drug

o Reactive functional groups such as alkyl halides may lead

to irreversible covalent bonds being formed between a
lead compound and its target.
 E.g. alkylation of macromolecular target by alkyl
halides
Q22.It is prohibited to remove the pharmacophore group in drug design. What
is pharmacophore group? State an alternative technique may you applied
instead of remove.

The pharmacophore summarizes the important groups which are

important in the binding of a lead compound to its target, as well as
their relative positions in three dimensions (for a specific
pharmacological activity).
o You may use masking the group if it provide bad odor or
making drug more soluble. Or shifting the group to make it
unrecognized by enzyme

Q23.list the strategies should be applied in optimizing the drug target

interactions and comment on each .

o Variation of substituents (alkyl and aromatic

substitution)
o Extension of structure (chain extension/contraction,
ring expansion/contraction),
o Ring variation,
o Ring fusion,
o Isostere and Bioisosteres,
o Simplification of the structure,
o Regidification of the structure.
o Conformational blocker
Q24.1. what are the techniques or strategies can you make to optimize the
access to the target?.

Controlling the comfortable ADME in drug designing

Q24.2. Give the technique can be performed in designing the following drugs

a) GIT drug
b) Drug for meningitis
c) Epileptic drug
d) Peripheral nerves drug
e) Iv injection drug
f) Topical drug or dermal drug
g) Transdermal drug

Q25.what is QSAR
The change in the polarity and ionization of compounds can be
altering their substituents

Q26.you are designing a drug with improving absorption then you find the
functional group you need to remove or mask involves in binding , How can
you overcome this issue?
o Adding non-polar molecules such as alkyl

Q27. Which is absorbed better than other and why ?

Q29.with examples, what are stereoelectronic modification?

o Involve steric effect

o And electronic effect by bioisostere

Q30.metabolic blockers
Q31. List the techniques involve in metabolism improvement. Discuss each

o Steric shields
o Electronic effects of Bioisosteres
o Stereoelectronic modification
o Metabolic Blocker
o Removal of susceptible metabolic groups
o Group Shifts
o Ring Variation

Q32.what is self-destruct drug

o A self-destruct drug is one which is chemically stable under

one set of conditions but becomes unstable and spontaneously
degrades under another set of conditions.
PART III. DRUG TARGET

Q33.Discuss the following regarding drug target

o How can design carcinogenic drug
o Drugs can be linked to amino acids or nucleic acid bases to target them
o How can you design drug target GIT infection
o Drugs can be targeted to the GIT by making them ionized or highly polar such that
they cannot cross the gut wall.
o How can you design epileptic drug
o The CNS side effects of peripherally acting drugs can be eliminated by
making the drugs more polar so that they do not cross the blood-brain
barrier

Q35.Regarding toxicity
Q36.what is prodrug

o Pro-drugs are compounds which are inactive in vitro and

converted in the body to active drug.

Q37. What are the purposes of prodrug in both pharmaceutical drug designing
and drug formulation processes?

To overcome the following problem

 Acid sensitivity
 Poor membrane permeability: to make it less polar
 Drug toxicity & side effects
 Bad taste
 Short duration of action
 Solubility
 Stability

Q38. All prodrug are activated by the enzyme? Explain

o Not all prodrugs are activated by metabolic enzymes.

o E.g. photodynamic therapy involves the use of an external
light source to activate prodrugs

Q39. With an examples , What is sentry drug

PART IV DRUG DEVELOPMENT
Q40.What are the three main issue involve in drug development?

 The drug has to be tested to ensure that it is not only safe and
effective, but can be administered in a suitable fashion.
o This involves preclinical and clinical trials covering toxicity,
drug metabolism, stability, formulation, and
pharmacological tests.

 There are the various patenting and legal issues.

 The drug has to be synthesized in ever-increasing quantities for
testing and eventual manufacture (this is known as chemical and
process development).
Q41. Regarding the drug development differentiate the chemical development
from process development.

o Chemical development aim to develop a synthetic route which

is straightforward, safe, cheap, and efficient, has the minimum
number of synthetic steps, and provide a consistency good
yield of high-quality product that meets predetermined purity
specifications.

o Process development aims to develop a production process

which is safe, efficient, economic, environmentally friendly,
and produces product of a consistent yield and quality to
satisfy purity specification.
Q42.what is an orphan drug?

Q43What does patent cover in drug development

Q44. You are analyzing the toxicity in vivo of the drug in animal. Give two
sample can be used to make analysis

Q45. What should you have to study in development of the drug

 Drug toxicology test and Drug Pharmacology [PK and PD]test
 Drug Formulation
Q46.National Institute of Health organize the clinical trial into 5 different type,
What are they???

 Treatment trials: test experimental treatments or a new combination of drugs.

 Prevention trials: look for ways to prevent a disease or prevent it from returning.
 Diagnostic trials: find better tests or procedures for diagnosing a disease.
 Screening trials: test methods of detecting diseases.
 Quality of Life trials: explore ways to improve comfort and quality of life for
individuals with a chronic illness.

Q47. Describes the phases of clinical trial.

QQ. the structure of aspirin is shown below , answer the questions

a) Explain why old tablets of aspirin that have been left in moist
air smell of vinegar.
b) Explain why aspirin is not very soluble in water.
c) Explain why aspirin is much more soluble in sodium
hydroxide solution than it is in water.
d) Write a chemical equation to show how soluble aspirin is
produced.
e) Explain what happens when soluble aspirin enters the
stomach.

QQ. What are the technique used in drug design

 3D structure of biological target( receptor-based drug design)
 Structure of known active small molecules( pharmacophore-based drug design).
 Computer assisted drug design (CADD)
 Molecular graphics
 Pattern recognition
 Receptor fit
 PREPARED BY MINANI THEOBALD
MODULE: BIOTECHNOLOGY AND DRUG DESIGN
SUBMODULE: DRUG DESIGN
YEAR OF STUDY: YEAR 2
DEPARTMENT OF PHARMACY
HUNIVERITY OF RWANDA

References
1.University Of Rwanda Lecturer’s notes updates 2016-17

2. Medicinal Chemistry and Drug Design, Edited by Deniz Ekinci

Published by InTech, Janeza Trdine 9, 51000 Rijeka, Croatia, Copyright © 2012 InTech

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